He first reached the major leagues with the Braves in 2005. Used exclusively as a reliever in the majors after being a starter in the minors, he had a solid rookie season, going 4-2, 3.11 in 43 games. However, his career after that has been even more of a roller coaster than the typical reliever's. He pitched for the Braves every season between 2005 and 2009, but an injury in 2006 limited him to two-thirds of an inning, and then he spent most of 2007 as a swingman with the AAA Richmond Braves before returning to Atlanta for 5 late-season appearances. In 2008, he made 76 appearances for the Braves, second on the team behind Will Ohman, but his record was a disappointing 2-6, 5.88. He was then traded to the St. Louis Cardinals for Brian Barton on April 20, 2009, but after 15 games with the Cards, he was placed on waivers and claimed by the Arizona Diamondbacks in early June. Between the three teams, he went 0-2, 4.12 in 48 games.

In 2010, he pitched 54 times for the Diamondbacks, with a record of 3-2, 4.26, then joined the New York Mets as a free agent in 2011. Things did not go well as his ERA shot up to 10.80 in 5 appearances and he almost completely washed out of baseball. He pitched with two other organizations that season, the Cardinals and the Pittsburgh Pirates, but this nightmarish year included putting up ERAs of 13.50 with both the Indianapolis Indians and Memphis Redbirds. He then missed all of 2012 with an injury, started 2013 in AAA with Omaha Storm Chasers before being sold to the Hanshin Tigers of Japan's Pacific League. He pitched well in 22 games there, however, going 3-1, 2.67, which rekindled interest in him back in the United States.

Boyer signed with the San Diego Padres for the 2014 season and began the year in AAA with the El Paso Chihuahuas. He went 1-2, 3.10 with 7 saves in 25 games to finally earn another look at the majors, over four years after his last appearance with the Mets. He continued to pitch well, going 0-1, 3.57 in 32 games with the Friars. Now reestablished as a legitimate major league reliever, he moved to the Minnesota Twins for 2015 and put up a solid 2.49 ERA in 68 games, in spite of a 3-6 record. He was one of the main set-up men for closer Glen Perkins and recorded 19 holds. In 2016, he moved again, this time to the Milwaukee Brewers.

In his spare time, Boyer has been involved with the Christian organization Exodus Road, whose purpose is to free young persons who have been used as sex slaves around the world. Former Braves teammate Adam LaRoche was also involved in the project. In addition to providing financial support, Boyer spent ten days overseas after the 2015 season working to free underage women working in brothels. Because of the danger of the work and the risk of reprisals from organized crime, he did not tell reporters about his activities at the time, and remained vague when prodded after LaRoche's controversial retirement from the game in the spring of 2016 brought their common activity to light.